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Repetitive transcranial magnetic stimulation (rTMS) and intensive cognitive rehabilitation (CR) were administered to two patients with cognitive dysfunction following brain injury. The first case was a 67-year-old man who presented with memory dysfunction, attention dysfunction, and decreased insight following diffuse axonal injury. High-frequency rTMS (10 Hz, 2400 pulses/day) targeting the anterior cingulate using a navigation system and CR were administered for 12 days at 1 year from the onset of injury. The patient showed improved neuropsychological performance and activities of daily living. In addition, single photon emission computer tomography with 99mTc-ECD showed improved perfusion in the anterior cingulate gyrus. The second case was a 68-year-old man who presented with dysfunction of memory, attention, and executive function following a cerebral infarction in the middle cerebral artery region within the right hemisphere. This patient received 12 days (except for Sundays) of low-frequency rTMS (1 Hz, 1200 pulses/day) targeting the left dorsolateral prefrontal cortex and the left posterior parietal cortex and CR. Following this intervention, the patient’s neuropsychological performance and activities of daily living improved. Furthermore, single photon emission computer tomography showed changes in perfusion in the rTMS target sites and areas surrounding the targets. We have shown the safety and efficacy of rTMS therapy using a navigation system combined with intensive CR on two patients with cognitive dysfunction following brain injury. In addition, we observed changes in the areas around the rTMS target sites in brain imaging data.